The rep gene of Porcine circovirus type 1 directs the synthesis of two proteins. The full-length protein Rep is 312 amino acids in size, the spliced variant Rep' is truncated (168 aa) and exon 2 is frame-shifted. Replication of PCV1 DNA depends on synthesis of both proteins. Rep and Rep' bind in vitro to double-stranded DNA fragments comprising part of the origin of replication of PCV1, but the minimal binding sites of the two proteins are distinct. Rep protein represses the promoter of the rep gene by binding to the two inner hexamers H1 and H2. Although Rep' binds to the same sequence, it does not influence Prep. Twelve hours after PCV1 infection, similar amounts of rep and rep' were detected by real-time PCR, but later on, the ratio of the two transcripts varied. Both proteins are co-localised in the nucleus and formation of homo- and heteromeric complexes has been observed. When a replication assay was performed, in which Rep and Rep' protein of PCV1 was used to replicate the origin of PCV1 and PCV2, the rep gene products were found to initiate replication at both origins of replication.